| --- |
| license: other |
| license_name: warwick-tia-citation-required |
| task_categories: |
| - image-segmentation |
| tags: |
| - medical |
| - histopathology |
| - ihc |
| - immunohistochemistry |
| - lymphocytes |
| - nuclei |
| - nuclick |
| pretty_name: NuClick-IHC |
| --- |
| |
| # NuClick-IHC (Lymphocyte Segmentation in IHC) |
|
|
| Immunohistochemistry (IHC) stained histopathology patches of lymphocytes with |
| per-nucleus instance segmentation masks. Released by the Warwick TIA Centre as |
| the IHC component of the NuClick framework's training/validation data, with |
| ROIs sourced from the LYON19 cohort (CD3/CD8 IHC of breast, colon, prostate). |
|
|
| ## Overview |
| - **Modality:** Histopathology (IHC, RGB microscopy) |
| - **Tissue:** Lymphocytes in CD3/CD8-stained breast/colon/prostate |
| - **Image size:** 256x256 RGB |
| - **Samples:** 671 train + 200 validation = 871 |
| - **Ground truth:** Per-nucleus instance segmentation masks generated by the |
| NuClick interactive tool and refined for training. The paper validates these |
| by showing a model trained on them placed first on LYON19. |
|
|
| ## Columns |
| | Column | Type | Notes | |
| |---|---|---| |
| | `id` | string | ROI identifier (e.g. `ROI_100_1`) | |
| | `image` | Image (RGB) | 256x256 IHC patch | |
| | `mask` | Image (mode `L`) | 256x256 uint8 instance map: 0 = background, 1..N = instance IDs | |
| | `num_nuclei` | int32 | Number of nuclei instances in the patch (0 if empty) | |
|
|
| ## Notes |
| - Approximately 30% of training patches and 25% of validation patches contain |
| no nuclei (`num_nuclei == 0`, mask is all-zero). This matches the source |
| release. |
| - Max instances per patch in this release is 69, so a uint8 mask losslessly |
| preserves all instance IDs. |
| - For semantic (foreground/background) use, threshold the mask with `mask > 0`. |
|
|
| ## Derivation |
| Source: `ihc_nuclick.zip` from https://warwick.ac.uk/fac/cross_fac/tia/data/nuclick/ |
| (IHC subset). The source ships 256x256 PNG images and uint32 .npy instance |
| maps; we re-encode masks as uint8 PNG (lossless under the observed instance |
| count). The companion `IHC_xml_asap/` folder contains the raw ASAP-compatible |
| polygon annotations and is not included here. |
| |
| ## License |
| The Warwick TIA release does not provide an explicit dataset license. Users |
| must cite the NuClick paper when publishing work derived from it. |
| |
| ## Citation |
| - Alemi Koohbanani N., Jahanifar M., Zamani Tajadin N., Rajpoot N. *NuClick: A |
| deep learning framework for interactive segmentation of microscopic images.* |
| Medical Image Analysis, 65:101771, 2020. doi:10.1016/j.media.2020.101771 |
| |
